Download an application called InstEd.
This will allow you to generate a Transform File against an MSI.
Basically you keep the MSI intact but the Transform Files has all your changes.
For example, here is one of ours for installing TeamViewer v15.
Note I have blurred out some account info.
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Then when I install the application I just reference that Transform File.
msiexec.exe /i "{PackageShare}\Teamviewer\MSI\TeamViewer_Host.v15.msi" /norestart /qn TRANSFORMS="{PackageShare}\Teamviewer\MSI\TeamViewer_Host.v15.Settings.mst"